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UNIVERSITY OF SANTO TOMAS

FACULTY OF PHARMACY


A Syllabus for the Organic Chemistry Lecture
First Semester AY 2012-2013

Course Title: ORGANIC CHEMISTRY LECTURE
Course Number: CHEM 200
Course Description: Introduces students to organic chemistry as a discipline. Deals with the different classes of organic compounds, their structures,
properties, reactivities, and reaction mechanisms. Students are expected to apply chemistry concepts in the different biochemical
and health-related fields of study.

Course Credit: 3 units

Contact Hours: 3 lecture hours per week

Prerequisite: General Inorganic Chemistry (CHEM 100)

Placement: Second Year, First Semester

General Objectives: 1. Analyze the behavior of organic molecules through the forces that hold different molecules or different parts of the same
molecule.
2. Predict the reactivities of different organic compounds based on structural concepts.
3. Apply general equations and principles to problems in medicine and agriculture.
4. Establish rationale for different laboratory and cellular observations in terms of the structural theory of organic chemistry.

FIRST GRADING PERIOD
Specific Objectives Topics
Time
Allotment
(Hrs)
Teaching
Strategies
Skills Values
Evaluation/
Assessment




1. Describe the atomic structure
and atomic orbitals
2. Differentiate ionic from covalent
bonds
3. Calculate the formal charge of
the atom
4. Describe the hybridization of
atoms present in simple organic

Unit 1: Structure and Bonding;
Acids and Bases

Atomic structure; atomic orbitals
Chemical bonds


Formal charge

Hybridization





5





Lecture
discussion
with the use of
3-dimensional
models






Critical
thinking,
Knowledge-
based,
Problem
solving




Honesty
Self-reliance
Diligence
Responsibility




Graded
recitation

Short quiz/es

Chapter quiz


2
compounds
5. Predict the direction of polarity of
a bond
6. Discuss the different structural
effects
7. Classify molecule as a Lewis
acid or a Lewis base
8. Illustrate the effect of structure
on pKa and the effect of pH on
the structure of an organic
compound

Bond polarity and
electronegativity
Structural effects

Lewis acids and Lewis bases

K
a
, pK
a
, K
b
, pK
b
, pH




1. Identify functional groups in
organic molecules
2. Illustrate the different kinds of
formulas
3. Differentiate all types of isomers
4. Classify the different types of
carbon atoms
5. Discuss the properties and
conformations of alkanes and
cycloalkanes


Unit 2: Alkanes:The Nature of
Organic Molecules

Functional groups

Different kinds of formulas

Isomers
Types of carbon atoms

Boiling/melting points; solubility
Conformations of alkanes and
cycloalkanes




5




Lecture
discussion
with the use of
PowerPoint
presentation
and 3-
dimensional
models





Critical
thinking,
Knowledge-
based




Honesty
Self-reliance
Diligence
Responsibility




Online quiz
Short quiz/es
Chapter quiz





1. Name and draw alkenes and
cycloalkenes
2. Explain cis-trans isomers of
alkenes
3. Assign E,Z configurations to
double bonds
4. Classify organic reactions
5. Discuss the roles of radicals,
nucleophiles and electrophiles in
organic reactions
6. Formulate the mechanism of
electrophilic addition reactions

Unit 3: Alkenes and Alkynes:
The Nature of Organic
Reactions

Electronic structure of alkenes

Cis-trans isomers of alkenes

Sequence rules of E,Z
designation
Kinds of organic reactions
Organic reaction intermediates


Electrophilic addition reaction






5









Blackboard e-
learning
module

Use of 3-
dimensional
models






Critical
thinking,
Knowledge-
based,
Technical,
Analytical





Hypothetical
reasoning
Honesty
Self-reliance
Diligence
Responsibility





Online quiz
Short quiz/es
Chapter quiz


3
7. Label a reaction energy diagram Reaction energy diagrams and
transition states
3 hrs. lec MONTHLY EXAMINATION

SECOND GRADING PERIOD




1. Predict the product of reactions
of alkenes, dienes and alkynes

2. Demonstrate correct preparation
of alkenes and alkynes
3. Describe the acidity of alkynes
4. Use the different reactions to
determine the structure of an
unknown compound

Unit 4: Reactions of Alkenes
and Alkynes

Reactions of alkenes, dienes, and
alkynes

Preparation of alkenes and
alkynes
Alkyne acidity
Structure elucidation




4




Lecture
discussion
with the use of
powerpoint
presentation
and 3-
dimensional
models





Critical
thinking,
Knowledge-
based




Honesty
Self-reliance
Diligence
Responsibility





Short quiz/es
Chapter quiz




1. Determine whether a substance
is aromatic or antiaromatic
2. Formulate the mechanisms of
electrophilic aromatic substitution
reactions
3. Predict the reactivity and
orientation of the aromatic ring
and substituents in electrophilic
aromatic substitution reactions
4. Discuss aromaticity in
nonbenzene rings and polycyclic
compounds
5. Synthesize substituted benzenes
through various reaction
pathways.

Unit 5: Aromatic Compounds

Benzene structure and stability
Aromaticity and Antiaromaticity
Electrophilic aromatic substitution
reactions of benzene

Substituent effects in electrophilic
aromatic substitutions


Polycyclic aromatic compounds


Organic synthesis



6



Lecture
discussion
with the use of
powerpoint
presentation


Blackboard e-
learning
module



Critical
thinking,
Knowledge-
based,
Analytical,
Technical



Hypothetical
reasoning
Honesty
Self-reliance
Diligence
Responsibility



Short quiz/es
Chapter quiz

4




1. Discuss chirality and optical
activity
2. Locate stereocenters in
molecules
3. Differentiate enantiomers from
diastereomers; meso
compounds from racemic
mixture
4. Describe stereochemistry of
reactions

Unit 6: Stereochemistry at
Tetrahedral Centers

Chirality and optical activity

Stereocenter

Enantiomers and diastereomers
Meso compounds and racemic
mixture

Chiral environment




2





Lecture
discussion
with the use of
powerpoint
presentation
and 3-
dimensional
models





Critical
thinking,
Knowledge-
based




Honesty
Self-reliance
Diligence
Responsibility




Short quiz/es
Chapter quiz






1. Illustrate the mechanisms of S
N
1
and S
N
2 reactions
2. Differentiate S
N
1 from S
N
2
reactions
3. Describe elimination reactions:
E1 and E2
4. Identify reactions as S
N
1, S
N
2,
E1, E1cB and E2
5. Predict the products of reactions
of alkyl halides and the effects of
changes in reaction conditions
on substitution and elimination
reactions

Unit 7: Organohalides:
Nucleophilic Substitutions and
Eliminations

Mechanisms of S
N
2 and S
N
1
reactions
Comparison of S
N
2 and S
N
1
reactions
Elimination reactions: E2, E1
and E1cB
Competition between substitution
and elimination






3










Lecture
discussion
with the use of
powerpoint
presentation






Critical
thinking,
Knowledge-
based,
Analytical,
Technical





Honesty
Self-reliance
Diligence
Responsibility





Short quiz/es
Chapter quiz




3 hrs. lec PRELIMINARY EXAMINATION










5

THIRD GRADING PERIOD





1. Differentiate alcohols from
phenols; ethers from epoxides;
and thiols from sulfides
2. Compare the properties of
alcohols, phenols, and ethers
3. Synthesize alcohols, ethers, and
phenols
4. Predict the products of reactions
involving alcohols, phenols, and
ethers

Unit 8: Alcohols, Phenols,
Ethers and Their Sulfur
Analogs

Alcohols, phenols, ethers,
epoxides, thiols, and sulfides

Properties of alcohols, ethers and
phenols: H-bonding, acidity
Synthesis and reactions of
alcohols, phenols, and ethers






4





Lecture
discussion
with the use of
powerpoint
presentation





Critical
thinking,
Knowledge-
based,
Analytical,
Technical





Honesty
Self-reliance
Diligence
Responsibility





Short quiz/es
Chapter quiz






1. Compare the reactivities of
aldehydes with that of ketones
2. Discuss the different reactions of
aldehydes and ketones

Unit 9: Aldehydes and Ketones:
Nucleophilic Addition
Reactions

Electronic structure of carbonyl
group
Reactions of aldehydes and
ketones





4




Lecture
discussion
with the use of
powerpoint
presentation




Critical
thinking,
Knowledge-
based




Honesty
Self-reliance
Diligence
Responsibility




Short quiz/es
Chapter quiz






1. Identify carboxylic acids and
derivatives
2. Discuss the physical properties
of carboxylic acids and
derivatives
3. Compare reactivities of
carboxylic acids and derivatives
4. Formulate mechanisms of simple
nucleophilic acyl substitution
reactions

Unit 10: Carboxylic Acids and
Derivatives: Nucleophilic Acyl
Substitution Reactions

Nomenclature and structures of
carboxylic acids and derivatives
Physical properties of carbonyl
compounds; acidity and solubility

Reactivities of carboxylic acids
and Derivatives
Reactions of carboxylic acids and
derivatives





4










Lecture
discussion
with the use of
powerpoint
presentation






Critical
thinking,
Knowledge-
based,
Technical,
Analytical





Hypothetical
reasoning
Honesty
Self-reliance
Diligence
Responsibility





Short quiz/es
Chapter quiz



6






1. Discuss keto-enol tautomerism
of carbonyl compounds
2. Illustrate carbonyl condensation
reactions

Unit 11: Carbonyl Alpha-
Substitution Reactions
and Condensation
Reactions

Keto-enol tautomerism
Aldol and Claisen condensation
reactions







2







Lecture
discussion
with the use of
powerpoint
presentation

Blackboard e-
learning
module



Critical
thinking,
Knowledge-
based



Honesty
Self-reliance
Diligence
Responsibility



Short quiz/es
Chapter quiz






1. Differentiate 1
o
, 2
o
, 3
o
, and 4
o

amines
2. Evaluate the base strengths of
amines
3. Discuss the reactions and
synthesis of amines


Unit 12: Amines

Different types of amines

Basicity of amines

Reactions and synthesis of
amines



1







Lecture
discussion
with the use of
powerpoint
presentation




Critical
thinking,
Knowledge-
based





Honesty
Self-reliance
Diligence
Responsibility



Short quiz/es
Chapter quiz



3 hrs. lec FINAL EXAMINATION



GRADING SYSTEM:

Three grading periods:
20% first grading period
40% second grading period
40% third grading period
Each grading period consists of 40% quizzes, 50% long examinations and 10% class standing.








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COURSE REFERENCES:

Basic Readings: McMurry J. (2011). Fundamentals of Organic Chemistry. 7
th
ed. Thomson Brooks/Cole, Belmont, CA, USA.

Extended Readings: Bruice, Paula Y. (2006). Essential Organic Chemistry. 1st

ed. Pearson Prentice Hall. Upper Saddle River, NJ.
Hart H., Craine LE, Hart DJ, and Hadad CM. (2007). Organic Chemistry A Short Course. 12
th
ed. Houghton Mifflin
Company, NY, USA.
Lim-Sylianco, Clara Y. Principles of Organic Chemistry. 6
th
ed. Aurum Technical Books.
Solomons, T.W. Graham and Craig B. Fryhle. (2008). Organic Chemistry. 9
th
ed. John Wiley and Sons, Inc., New York.

Web Based: www.cengage.com/brookscole
www.thomsonedu.com
www.iupac.org
www.chem.qmul.ac.uk/iupac/
http://pubs.acs.org/journals/joceah/index.html
www.jbc.org/

Instructional Media: interactive animated discussion



Prepared by: Organic Chemistry Group (Department of Biochemistry)
March 29, 2012



Approved by:



Prof. Priscilla M. Torres, Ph.D.
Dean
April 15, 2012